Quick start guide

Adorym does 2D/3D ptychography, CDI, holography, and tomography all using the reconstruct_ptychography function in ptychography.py. You can make use of the template scripts in demos or tests to start your reconstruction job.

Running a demo script

Adorym comes with a few datasets and scripts for demonstration and testing, but the raw data files of some of them are stored elsewhere due to the size limit on GitHub. If the folder in demos or tests corresponding to a certain demo dataset contains only a text file named raw_data_url.txt, please download the dataset at the URL indicated in the file.

On your workstation, open a terminal in the demos folder in Adorym’s root directory, and run the desired script – say, multislice_ptycho_256_theta.py, which will start a multislice ptychotomography reconstruction job that solves for the 256x256x256 “cone” object demonstrated in the paper (see Publications), with

python multislice_ptycho_256_theta.py

To run the script with multiple processes, use

mpirun -n <num_procs> python multislice_ptycho_256_theta.py

Running your own jobs

You can use the scripts in demos and tests as templates to create the scripts for your own jobs. While the major API is the function reconstruct_ptychography itself, you may also explicitly declare optimizers to be used for the object, the probe, and any other refinable parameters. Below is an example script used for 2D fly-scan ptychography reconstruction with probe position refinement:

To learn the settings of the reconstruct_ptychography function and the expected HDF5 format, please visit Usage.